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PhD Defense - Irena Lanc

Start: 6/16/2014 at 11:50AM
End: 6/16/2014 at 5:00PM
Location: 315 Stinson Remick
Attendees: Faculty and students are welcome to attend the presentation portion of the defense. Light refreshments will be served.
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Irena Lanc

PhD Candidate

June 16, 2014, 315 Stinson Remick, 1:00pm


Dr. Scott Emrich

Committee Members:

Dr. Kevin Bowyer     Dr. Michael Pfrender      Dr. Douglas Thain


“Novel Methods for Assembly Validation and Improvement”


Advancements in sequencing technology have made it possible to acquire large amounts of genomic data in a relatively cost-effective fashion. However, accurate and reliable genome assembly remains a challenge. The work presented here aims to facilitate both the validation and the correction of assemblies. The validation method was developed to locate putative  assembly errors by gathering detailed quantitative information about each section of the assembly, and isolating the suspected misassemblies through the use of unsupervised learning algorithms. The data gathered during validation is then exploited in a second application designed for assembly correction. It is used to guide the process of meta-assembly, wherein two different assemblies are merged to produce a final sequence of greater quality. Supplementing the meta-assembly with detailed quality information allows for a more informed combination of sequences from each constituent assembly, resulting in a more accurate final product. Together, these applications aim to highlight the importance of incorporating sequence quality into assembly. The detailed detection of anomalous sequences, when combined with the capacity to also improve the assemblies, can enable the construction of more robust and correct assemblies.